data_1GFI
#
_model_server_result.job_id            AnnFrr8yYhEEYHnc3GY8LA 
_model_server_result.datetime_utc      '2024-10-18 17:21:13' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          1gfi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":355}' 
#
_entry.id    1GFI 
#
_exptl.entry_id    1GFI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            1GFI 
_cell.length_a            80.5 
_cell.length_b            80.5 
_cell.length_c            106.55 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1GFI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OG SER 46 A SER 47 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc2 A OG1 THR 180 A THR 181 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc3 D O2B GDP . A GDP 355 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc4 D O3B GDP . A GDP 355 1_555 C AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc5 D O1B GDP . A GDP 355 1_555 C AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.701 ? 
metalc ? metalc6 D O2B GDP . A GDP 355 1_555 C AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.608 ? 
metalc ? metalc7 B MG MG . A MG 356 1_555 C F3 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc8 B MG MG . A MG 356 1_555 C AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.567 ? 
metalc ? metalc9 B MG MG . A MG 356 1_555 E O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc10 B MG MG . A MG 356 1_555 E O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc11 C AL ALF . A ALF 357 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PB O1B GDP doub 87 n n 
PB O2B GDP sing 88 n n 
PB O3B GDP sing 89 n n 
PB O3A GDP sing 90 n n 
O2B HOB2 GDP sing 91 n n 
O3B HOB3 GDP sing 92 n n 
O3A PA GDP sing 93 n n 
PA O1A GDP doub 94 n n 
PA O2A GDP sing 95 n n 
PA O5' GDP sing 96 n n 
O2A HOA2 GDP sing 97 n n 
O5' C5' GDP sing 98 n n 
C5' C4' GDP sing 99 n n 
C5' H5' GDP sing 100 n n 
C5' "H5''" GDP sing 101 n n 
C4' O4' GDP sing 102 n n 
C4' C3' GDP sing 103 n n 
C4' H4' GDP sing 104 n n 
O4' C1' GDP sing 105 n n 
C3' O3' GDP sing 106 n n 
C3' C2' GDP sing 107 n n 
C3' H3' GDP sing 108 n n 
O3' HO3' GDP sing 109 n n 
C2' O2' GDP sing 110 n n 
C2' C1' GDP sing 111 n n 
C2' H2' GDP sing 112 n n 
O2' HO2' GDP sing 113 n n 
C1' N9 GDP sing 114 n n 
C1' H1' GDP sing 115 n n 
N9 C8 GDP sing 116 n y 
N9 C4 GDP sing 117 n y 
C8 N7 GDP doub 118 n y 
C8 H8 GDP sing 119 n n 
N7 C5 GDP sing 120 n y 
C5 C6 GDP sing 121 n n 
C5 C4 GDP doub 122 n y 
C6 O6 GDP doub 123 n n 
C6 N1 GDP sing 124 n n 
N1 C2 GDP sing 125 n n 
N1 HN1 GDP sing 126 n n 
C2 N2 GDP sing 127 n n 
C2 N3 GDP doub 128 n n 
N2 HN21 GDP sing 129 n n 
N2 HN22 GDP sing 130 n n 
N3 C4 GDP sing 131 n n 
#
_atom_sites.entry_id                     1GFI 
_atom_sites.fract_transf_matrix[1][1]    0.012422 
_atom_sites.fract_transf_matrix[1][2]    0.007172 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014344 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009385 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 MG A 1 356 356 MG MG . 
C 3 ALF A 1 357 357 ALF ALF . 
D 4 GDP A 1 355 355 GDP GDP . 
E 5 HOH A 1 401 401 HOH HOH . 
E 5 HOH A 2 402 402 HOH HOH . 
E 5 HOH A 3 403 403 HOH HOH . 
E 5 HOH A 4 404 404 HOH HOH . 
E 5 HOH A 5 405 405 HOH HOH . 
E 5 HOH A 6 406 406 HOH HOH . 
E 5 HOH A 7 407 407 HOH HOH . 
E 5 HOH A 8 408 408 HOH HOH . 
E 5 HOH A 9 409 409 HOH HOH . 
E 5 HOH A 10 410 410 HOH HOH . 
E 5 HOH A 11 411 411 HOH HOH . 
E 5 HOH A 12 412 412 HOH HOH . 
E 5 HOH A 13 413 413 HOH HOH . 
E 5 HOH A 14 414 414 HOH HOH . 
E 5 HOH A 15 415 415 HOH HOH . 
E 5 HOH A 16 416 416 HOH HOH . 
E 5 HOH A 17 417 417 HOH HOH . 
E 5 HOH A 18 418 418 HOH HOH . 
E 5 HOH A 19 419 419 HOH HOH . 
E 5 HOH A 20 420 420 HOH HOH . 
E 5 HOH A 21 421 421 HOH HOH . 
E 5 HOH A 22 422 422 HOH HOH . 
E 5 HOH A 23 423 423 HOH HOH . 
E 5 HOH A 24 424 424 HOH HOH . 
E 5 HOH A 25 425 425 HOH HOH . 
E 5 HOH A 26 426 426 HOH HOH . 
E 5 HOH A 27 427 427 HOH HOH . 
E 5 HOH A 28 428 428 HOH HOH . 
E 5 HOH A 29 429 429 HOH HOH . 
E 5 HOH A 30 430 430 HOH HOH . 
E 5 HOH A 31 431 431 HOH HOH . 
E 5 HOH A 32 432 432 HOH HOH . 
E 5 HOH A 33 433 433 HOH HOH . 
E 5 HOH A 34 434 434 HOH HOH . 
E 5 HOH A 35 435 435 HOH HOH . 
E 5 HOH A 36 436 436 HOH HOH . 
E 5 HOH A 37 437 437 HOH HOH . 
E 5 HOH A 38 438 438 HOH HOH . 
E 5 HOH A 39 439 439 HOH HOH . 
E 5 HOH A 40 440 440 HOH HOH . 
E 5 HOH A 41 441 441 HOH HOH . 
E 5 HOH A 42 442 442 HOH HOH . 
E 5 HOH A 43 443 443 HOH HOH . 
E 5 HOH A 44 444 444 HOH HOH . 
E 5 HOH A 45 445 445 HOH HOH . 
E 5 HOH A 46 446 446 HOH HOH . 
E 5 HOH A 47 447 447 HOH HOH . 
E 5 HOH A 48 448 448 HOH HOH . 
E 5 HOH A 49 449 449 HOH HOH . 
E 5 HOH A 50 450 450 HOH HOH . 
E 5 HOH A 51 451 451 HOH HOH . 
E 5 HOH A 52 452 452 HOH HOH . 
E 5 HOH A 53 453 453 HOH HOH . 
E 5 HOH A 54 454 454 HOH HOH . 
E 5 HOH A 55 455 455 HOH HOH . 
E 5 HOH A 56 456 456 HOH HOH . 
E 5 HOH A 57 457 457 HOH HOH . 
E 5 HOH A 58 458 458 HOH HOH . 
E 5 HOH A 59 459 459 HOH HOH . 
E 5 HOH A 60 460 460 HOH HOH . 
E 5 HOH A 61 461 461 HOH HOH . 
E 5 HOH A 62 462 462 HOH HOH . 
E 5 HOH A 63 463 463 HOH HOH . 
E 5 HOH A 64 464 464 HOH HOH . 
E 5 HOH A 65 465 465 HOH HOH . 
E 5 HOH A 66 466 466 HOH HOH . 
E 5 HOH A 67 467 467 HOH HOH . 
E 5 HOH A 68 468 468 HOH HOH . 
E 5 HOH A 69 469 469 HOH HOH . 
E 5 HOH A 70 470 470 HOH HOH . 
E 5 HOH A 71 471 471 HOH HOH . 
E 5 HOH A 72 472 472 HOH HOH . 
E 5 HOH A 73 473 473 HOH HOH . 
E 5 HOH A 74 474 474 HOH HOH . 
E 5 HOH A 75 475 475 HOH HOH . 
E 5 HOH A 76 476 476 HOH HOH . 
E 5 HOH A 77 477 477 HOH HOH . 
E 5 HOH A 78 478 478 HOH HOH . 
E 5 HOH A 79 479 479 HOH HOH . 
E 5 HOH A 80 480 480 HOH HOH . 
E 5 HOH A 81 481 481 HOH HOH . 
E 5 HOH A 82 482 482 HOH HOH . 
E 5 HOH A 83 483 483 HOH HOH . 
E 5 HOH A 84 484 484 HOH HOH . 
E 5 HOH A 85 485 485 HOH HOH . 
E 5 HOH A 86 486 486 HOH HOH . 
E 5 HOH A 87 487 487 HOH HOH . 
E 5 HOH A 88 488 488 HOH HOH . 
E 5 HOH A 89 489 489 HOH HOH . 
E 5 HOH A 90 490 490 HOH HOH . 
E 5 HOH A 91 491 491 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PB GDP . . . D 4 36.574 -30.873 10.195 1 9.1 ? PB GDP 355 A 1 
HETATM 2 O O1B GDP . . . D 4 36.128 -31.749 9.126 1 11.23 ? O1B GDP 355 A 1 
HETATM 3 O O2B GDP . . . D 4 35.495 -30.067 10.819 1 13.09 ? O2B GDP 355 A 1 
HETATM 4 O O3B GDP . . . D 4 37.673 -31.465 10.982 1 16.8 ? O3B GDP 355 A 1 
HETATM 5 O O3A GDP . . . D 4 37.373 -29.726 9.407 1 9.55 ? O3A GDP 355 A 1 
HETATM 6 P PA GDP . . . D 4 37.62 -28.148 9.591 1 8.94 ? PA GDP 355 A 1 
HETATM 7 O O1A GDP . . . D 4 36.431 -27.44 9.073 1 9.32 ? O1A GDP 355 A 1 
HETATM 8 O O2A GDP . . . D 4 38.105 -27.828 11.012 1 9.14 ? O2A GDP 355 A 1 
HETATM 9 O O5' GDP . . . D 4 38.752 -27.862 8.522 1 7.57 ? O5' GDP 355 A 1 
HETATM 10 C C5' GDP . . . D 4 40.194 -28.024 8.713 1 9.36 ? C5' GDP 355 A 1 
HETATM 11 C C4' GDP . . . D 4 41.067 -26.876 8.194 1 5.41 ? C4' GDP 355 A 1 
HETATM 12 O O4' GDP . . . D 4 41.046 -26.77 6.711 1 9.16 ? O4' GDP 355 A 1 
HETATM 13 C C3' GDP . . . D 4 40.647 -25.513 8.782 1 6.36 ? C3' GDP 355 A 1 
HETATM 14 O O3' GDP . . . D 4 41.772 -24.711 9.157 1 9.19 ? O3' GDP 355 A 1 
HETATM 15 C C2' GDP . . . D 4 40.039 -24.831 7.499 1 10.21 ? C2' GDP 355 A 1 
HETATM 16 O O2' GDP . . . D 4 40.194 -23.414 7.461 1 17.29 ? O2' GDP 355 A 1 
HETATM 17 C C1' GDP . . . D 4 40.773 -25.429 6.307 1 7.02 ? C1' GDP 355 A 1 
HETATM 18 N N9 GDP . . . D 4 39.822 -25.521 5.233 1 7.04 ? N9 GDP 355 A 1 
HETATM 19 C C8 GDP . . . D 4 38.566 -26.113 5.19 1 7.45 ? C8 GDP 355 A 1 
HETATM 20 N N7 GDP . . . D 4 38.055 -26.266 3.972 1 8.08 ? N7 GDP 355 A 1 
HETATM 21 C C5 GDP . . . D 4 39.062 -25.632 3.165 1 11.94 ? C5 GDP 355 A 1 
HETATM 22 C C6 GDP . . . D 4 39.166 -25.405 1.711 1 12.04 ? C6 GDP 355 A 1 
HETATM 23 O O6 GDP . . . D 4 38.393 -25.722 0.817 1 12.11 ? O6 GDP 355 A 1 
HETATM 24 N N1 GDP . . . D 4 40.331 -24.746 1.33 1 14.04 ? N1 GDP 355 A 1 
HETATM 25 C C2 GDP . . . D 4 41.375 -24.463 2.19 1 11.81 ? C2 GDP 355 A 1 
HETATM 26 N N2 GDP . . . D 4 42.338 -23.678 1.801 1 5.99 ? N2 GDP 355 A 1 
HETATM 27 N N3 GDP . . . D 4 41.365 -24.849 3.472 1 16.22 ? N3 GDP 355 A 1 
HETATM 28 C C4 GDP . . . D 4 40.149 -25.288 3.93 1 8.6 ? C4 GDP 355 A 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           28 
#